Breaking changes in Tifffile 2025.5.21

[erikogabrielsson]

Hi @ap--

I get ImportError for ZarrTiffStore with Tifffile 2025.5.21.

C:\Users\er-gac\AppData\Local\pypoetry\Cache\virtualenvs\wsidicomizer-7Tqls5mv-py3.11\Lib\site-packages\tiffslide\_zarr.py:17: in <module>
    from tifffile import ZarrTiffStore
E   ImportError: cannot import name 'ZarrTiffStore' from 'tifffile' (C:\Users\er-gac\AppData\Local\pypoetry\Cache\virtualenvs\wsidicomizer-7Tqls5mv-py3.11\Lib\site-packages\tifffile\__init__.py)

Looking at the changes there namespace change is obviously a problem. I'm not sure if the dropped support for Zarr 2 is a problem.

/Erik

[ap--]

Hi @erikogabrielsson

Thanks for reporting. I'll make an intermediate release with an upper bound for tifffile.

Fixing this correctly will require a tiffslide release with zarr3 and tifffile>=2025.5.21 as dependencies, which will need some refactoring. The easiest way would be to drop 3.9 and 3.10 support too for that one.

[ap--]

tiffslide v2.5.1 is released with the upper bound. I'll leave this open before a new version is released with zarr3 support.

[psobolewskiPhD]

I'm not sure exactly how you access the stores, but I was able to get napari-tiff to use either zarr2 or 3 with the right tifffile with no pins. See: https://github.com/napari/napari-tiff/pull/48

Mind you in my hands, performance is much worse with zarr3. see discussion following from: https://github.com/cgohlke/tifffile/issues/297#issuecomment-2905785157

[ap--]

Hi @erikogabrielsson and @psobolewskiPhD,

I worked on moving to newer tifffile and zarr v3 in https://github.com/Bayer-Group/tiffslide/pull/97 If you could give it a shot and let me know if that works for zarr v3 support you I can make a new release.

This will be a breaking change. so tiffslide v3.0.0